RealLine HIV quantitative Str-Format

Transcription

1 Instructions for use DETECTION AND QUANTIFICATION OF THE HUMAN IMMUNODEFICIENCY VIRUS RNA BY REAL TIME PCR Research Use Only (RUO) Attention! Please read the information about quantification process carefully! (Str-format) VBD Tests valid from September 2018 Rev08_0918_EN Page 1 of 12

2 Explanation of symbols used in labeling RUO LOT REF Σ For research use only Batch code Catalogue number Content of number of tests Expiry date Temperature limitation Consult instructions for use Manufacturer Keep out of sunlight BIORON Diagnostics GmbH Rheinhorststr Ludwigshafen (Germany) Phone Fax: Legals: Limited Product Warranty: This warranty limits our liability for the replacement of this product. No warranties of any kind, express or implied, including, without limitation, implied warranties of merchantability or fitness for a particular purpose, are provided. BIORON Diagnostics GmbH shall have no liability for any direct, indirect, consequential, or incidental damages arising out of the use, the results of use, or the inability to use this product. Trademarks: FAM, HEX, JOE and ROX are trademarks of Applera Corporation or its subsidiaries in the US and certain other countries. iq and CFX are trademarks of Bio-Rad Laboratories, Inc. Rotor-Gene is a registered trademark of Qiagen Group, Germany. Rev08_0918_EN Page 2 of 12

3 Table of content: 1. STORAGE AND TRANSPORTATION 4 2. KIT CONTENTS 4 3. INTRODUCTION 5 4. PRINCIPLES OF THE PROCEDURE 5 5. PRECAUTIONS 6 6. ADDITIONAL MATERIALS AND DEVICES REQUIRED BUT NOT SUPPLIED 6 7. REAGENT AND SAMPLE PREPARATION 7 8. PROCEDURE PROTOCOL 8 9. DATA ANALYSIS 9 ATTACHMENT 1: CALCULATION OF VIRAL RNA CONCENTRATION 11 ATTACHMENT 2: ANALYTICAL SYSTEM VALIDATION 11 VBD0195 Page 3 of 12

4 HUMAN IMMUNODEFICIENCY VIRUS (HIV) RNA REAL TIME PCR DETECTION AND QUANTIFICATION Research Use Only 1. INTRODUCTION Assay kit RealLine HIV Quantitative kit is intended for the quantitative detection of Human Immunodeficiency virus (HIV) RNA in plasma and serum. The method is based on the reverse transcription of viral RNA to generate complementary DNA (cdna), with subsequent amplification of target cdna by Polymerase Chain Reaction (PCR) with fluorescent detection of amplified DNA in the real-time mode. Assay kit is adapted for real-time PCR detection systems like RealLine Cyclers (BIORON Diagnostics GmbH), iq icycler, iq5 icycler, CFX96 (Bio-Rad, USA), DT-96 (DNA-Technology, Russia) or their analogues. The assay kit contains reagents sufficient for 96 test runs. For the quantification process use three replicas of Positive Control sample and one Negative Control sample in each test run. RealLine HIV is designed to detect HIV RNA isolated from serum (plasma) using RNA extraction kit: RealLine Extraction 100 or RealLine Extraction KIT CONTENTS Ready Master Mix for reverse transcription and PCR, freeze-dried (RMM) Recovery Solution for Control samples (RSC) Weak Positive Control Sample (WPC HBV/HCV/HIV), freeze-dried Positive Control (PC) sample, freeze-dried Samples for calibration Calibration Sample No 1 (CS1) Calibration Sample No 2 (CS2) freeze-dried are used when the adequacy of analytical system has to be checked, see the Attachment 2 Passport with the specific concentrations of controls 96 test tubes (12 strips 8 tubes) 2 vials 4 ml each 1 vial 2 vials 1 vial each Rev08_0918_EN Page 4 of 12

5 3. PRINCIPLES OF THE PROCEDURE Principle of analysis is based on the reverse transcription of viral RNA with subsequent PCR amplification of target cdna by PCR with fluorescence detection of amplified DNA in the real-time mode. Reliability of analysis is provided by application of Weak Positive Control sample. Quantification of Human Immunodeficiency virus RNA is provided by application of the Positive Control (PC) in each test run. Positive Control is characterized in international units (IU/ml) by World Health Organization (WHO international standard for Human Immunodeficiency virus NIBSC Code: 97/656), and serves as a Quantitation Standard for calculation of viral quantity. Threshold cycle value Ct is the cycle number at which fluorescence generated within a reaction crosses fluorescence threshold, a fluorescence signal significantly above the background fluorescence. Quantity of viral RNA in initial sample is calculated by comparison of the threshold cycle value of analyzed sample and Positive Control. Also efficiency of sample preparation and reverse transcription should be considered. 4. SPECIFICATION Specificity: The samples containing HIV RNA with concentration above the detection limit will be determined as positive. If specimen does not contain HIV RNA, analysis will give negative result (in 100% of cases). Dynamic range of estimated concentration (linearity area): from 20 IU/ml to 10 8 IU/ml HIV RNA for the RNA isolation from 1 ml of serum (plasma). 1 IU = 0.58 copies of HIV RNA (National Institute of Biological Standards and Control for WHO international standard for Human Immunodeficiency virus NIBSC Code: 97/656). Sensitivity: Assay kit securely determines HIV RNA in concentration not less than 20 IU/ml for the RNA isolation from 1 ml of serum (plasma). 5. STORAGE AND TRANSPORTATION Store assay kit at (2-8) С in the manufacturer s packing. Transportation up to 25 С for 10 days is allowed. Do not freeze reagents. Do not pool reagents from different lots or from different vials of the same lot. Strictly follow the Instruction manual for reliable results. VBD0195 Page 5 of 12

6 6. WARNING AND PRECAUTIONS For research use only. The kits must be used by skilled personnel only. When handling the kit, follow the national safety requirements for working with pathogens. To prevent contamination, the stages of RNA isolation and PCR test run must be spatially separated. Avoid microbial and nuclease contamination of reagents when removing aliquots from reagent vials. Wear protective disposable gloves, laboratory coats and eye protection when handling specimens and kit reagents. Every workplace must be provided with its own set of variable-volume pipettes, necessary auxiliary materials and equipment. It is prohibited to relocate them to other workplaces. The use of sterile disposable pipette tips is recommended. Never use the same tips for different samples. Do not pool reagents from different lots or from different vials of the same lot. Dispose unused reagents and waste in accordance with country, federal, state and local regulations. Do not use the kit after the expiration date at the label at the side of the box. 7. ADDITIONAL MATERIALS AND DEVICES REQUIRED BUT NOT SUPPLIED Real time PCR device RealLine Cycler (BIORON Diagnostics GmbH), iq/iq5 icycler, CFX96 (Bio-Rad, USA), DT-96 (DNA-technology, Russia) or equivalent; RNA Extraction Kit: RealLine Extraction 100 or RealLine Extraction 1000 Tubes or plates and PCR foils, if the delivered format is not matching with the used system. Disposable gloves, powder-free; Pipettes (capacity μl) with filters (aerosol barriers); Disposable DNAse/RNase-free tips with filters 0.2 ml microtube racks Razor or scalpel. If an extraction kit from another supplier is used: RealLine Internal Control (VBC8881) Negative Control (negatively controlled plasma) Rev08_0918_EN Page 6 of 12

7 8. REAGENT AND SAMPLE PREPARATION Each group of samples undergoing the procedure of NA isolation must include a Positive Control sample (PC) from this kit and a Negative Control sample (NC) which is a component of the NA extraction kit. We strongly recommend the implementation of the Internal Control IC, the Negative Control NC and Positive Control PC samples to the extraction procedure, for quantitative determination use 3 Positive Control Samples. When using a kit of another supplier for the extraction of nucleic acids as recommended in p1, add 20 μl of IC (VBC8881) to each tube. For NC use 100 µl of the Negative Control Sample For the PC use 70 μl of Negative Control Sample and 30 μl of Positive Control to the tube marked PC. 8.1 Sample preparation. Prepare specimens for the assay with Extraction kit RealLine Extraction 100 or RealLine Extraction 1000 according to Extraction kit manual. Note: For quantification process three replica of Positive Control sample and one Negative Control sample in each test run are necessary. Attention: In case of necessity to check the adequacy of analytical system, three replicas of both Calibration sample 1 and 2 (CS1 and CS2) should be used (see the Attachment 2), to confirm the correspondence between measured values and the passport. The analytical sensitivity can be monitored with the additional use of the WPC. The Ct-value should be less than 40. Preparation of Control samples: Add 1 ml of Recovery Solution for Control samples (RSC) into each vial with Positive Control (PC) sample and Weak Positive Control sample (WPC), mix gently, keep for 15 minutes, carefully mix once again. PC and WPC should be stored at (2-8) С and used within 1 month after preparation. 8.2 Reagent preparation Preparation of Ready Master Mix Prior to use, warm reagents (do not open!) at room temperature (18-25) С. Open the package, separate an appropriate number of reaction tubes with Ready Master Mix (RMM) using razor or scalpel. Keep the tubes not used for the test in the original bag. Squeeze air out of the bag before closing the clip. VBD0195 Page 7 of 12

8 9. PROCEDURE PROTOCOL 9.1 Place the tubes with processed specimens and controls to Magnetic Rack. 9.2 Prepare an appropriate number of reaction tubes with Ready Master Mix (RMM). Label each reaction tube for each patient specimen and control sample. Attention! Put marks on the lateral part of a reaction tube. 9.3 Add 50 μl of each processed specimen and control to the appropriately labeled reaction tube using a new RNase-free tip with aerosol barrier for each sample. Do not grasp sorbent particles! 9.4 Place reaction tubes into the thermal block of real time PCR device and program the settings respectively. Program real time PCR device as follows: Step 1: 50 C 2 min Step 2: 95 C 2 min Step 3: 94 C 10 sec 50 Cycles 60 C* 40 sec * measurement of fluorescent at 60 C in FAM and ROX Collect real-time PCR data through the FAM channel for detection of amplification of IC cdna. Collect real-time PCR data through the ROX channel for detection of amplification of HIV cdna. 9.5 Start the PCR Run Rev08_0918_EN Page 8 of 12

9 10. DATA ANALYSIS 10.1 Calculate (IC Ct)m as the average Ct value of IC for all samples (including PC and NC). Samples with Ct of IC, that differs from (IC Ct)m by more than 2, should be ignored. After screening, recalculate (IC Ct)m for remaining samples. If Ct of IC for such samples differs from (IC Ct)m by more than 2, then result for this sample should be considered as equivocal. The test should be repeated from the sample RNA extraction stage In Positive Control sample and Weak Positive Control sample (also for CS1 and CS2) the program should detect: ROX fluorescence signal increase and Сt value (HIV cdna amplification); FAM fluorescence signal increase and Сt value (IC cdna amplification) In Negative Control sample the program should detect: FAM fluorescence signal increase and Ct value, and no significant ROX fluorescence increase should appear. If Ct value for NC in ROX channel is less than 40, this indicates the presence of contamination. All positive results in this test should be repeated from the RNA extraction stage. Negative samples of such test runs are considered reliable The sample is considered positive if Ct value in the ROX channel does not exceed 40. If Ct of IC for this sample differs from (IC Ct)m more than 2, the sample is considered as positive without quantitative analysis. For quantitative analysis, repeat the test beginning from the RNA isolation stage The test results are considered reliable only when Positive and Negative controls perform as expected. Note: Recommended setting for the Threshold is up to 20 % of the PC or the highest fluorescence signal, especially in not validated cyclers. VBD0195 Page 9 of 12

10 Summary of results: PC NC Samples FAM IC ROX HIV Test Results + + Valid - - Not valid Repeat test + - Not valid Repeat test - + Questionable Check results, possibly repeat tests + - Valid - - Not valid Repeat test + + Not valid Repeat test, contamination - + Not valid Repeat test + Ct < 40 Valid Positive + - Or Valid Negative Ct > Not valid Repeat test - + Questionable Check results, possibly repeat test HIV quantitation analysis. For quantitative analysis calculate the HIV RNA concentration in analyzed samples in accordance with Attachment 1. Attention! For RNA isolation from 100 μl of sample result should be multiplied by 10. If calculated HIV RNA concentration is in dynamic range from 100 IU/ml to 10 8 IU/ml result should be reported as positive with indication of calculated HIV RNA concentration in the sample (in IU/ml). Test results higher than 10 8 IU/ml are above the upper limit of quantitation and should be reported as higher than 10 8 IU/ml. Test results lower than 100 IU/ml are below the lower limit of quantitation and should be reported as HIV RNA detected, lower than 100 IU/ml. An analyzed sample is considered as negative if the result does not obtain a Ct value along the ROX channel or the Ct value exceed 40. For further information and help, ask us at techsupport@bioron.de. We can provide you a calculation sheet for an easy evaluation of your data. Rev08_0918_EN Page 10 of 12

11 ATTACHMENT 1: CALCULATION OF VIRAL RNA CONCENTRATION Calculate the viral RNA concentration using the following equation: = ( ) ( ), Where: sample number; PC concentration, specified in the passport of assay kit; and Сt value of the PC sample ROX and FAM channels, accordingly; and Сt value of the sample numbered k along ROX and FAM channels, accordingly, if amplification efficiency is (Еа) =100%. ATTACHMENT 2: ANALYTICAL SYSTEM VALIDATION Calculation of viral RNA concentration for PC using calibration graph. For precise calculation of viral RNA concentration in analyzed samples, analytical system validation should be done by comparison of PC concentration, specified in the passport of Assay kit with PC concentration, calculated using calibration graph. This validation is just necessary for the first time using the kit and to check the system regularly. 1. Prior use, warm reagents at room temperature (18-25) С for 30 minutes. Prepare NC, PC and IC as recommended in the instruction. 2. Add 1 ml of Recovery Solution for Control samples (RSC) into a vial with Calibration sample 1 (CS1) and Calibration sample 2 (CS2). Mix gently, keep for 15 minutes, and carefully mix once again. 3. Prepare ml tubes one for NC, 3 repeats for each PC, CS1 and CS2. 4. Label one 2.0 ml tube for NC, and ml tubes each for PC, CS1 and CS2 5. Add 30 μl of IC to each tube. 6. For NC, add to the tube, marked NC, 1 ml (100 μl) of Negative Control. 7. For PC, add to each of three tubes, marked PC, 970 (70) μl of Negative Control, and 30 μl of Positive Control. 8. For CS1 add to each of three tubes marked CS1 970 (70) μl of Negative Control, and 30 μl of Calibration sample 1. VBD0195 Page 11 of 12

12 9. For CS2 add to each of three tubes marked CS2 970 (70) μl of Negative Control, and 30 μl of Calibration sample Run the isolation of NA as recommended in the instruction. 11. Run the PCR (or reversed PCR). 12. For each sample calculate correct Ct value, using the following equation: = ( ) Calculate average value for PC, CS1 and CS2 (,, ). Samples with, that differs from more then 2, should be ignored. After screening, recalculate for samples remained. 13. Calculate B coefficient for calculating of specific viral NA, using following equation: =!"( #)!"( ) $ $ # Where: % and % specific viral NA concentration in Calibration samples (specified in the passport of Assay kit); For amplification efficiency 100%: & = log 2 = 0,3 14. Using received results, calculate concentration of specific viral RNA for Positive Control sample, using the following analytical equation: = #-. (IU/ml) Where: /01 = log(% ) + & ( ) average Z value for Calibration Sample 1 repeats; average Z value for Positive Control sample repeats; 15. If the calculated value of specific viral RNA concentration in PC differs no more than 2 from the value specified in the passport of a set, PC can be used as the sample of comparison for the further calculations of specific viral RNA concentration in investigated samples. 16. With the calculated Efficiency factor B it is possible to use this value in the formula for concentration calculation. (Attachment 1) For further information and help, ask us at techsupport@bioron.de. We can provide you a calculation sheet for an easy evaluation of your data. Rev08_0918_EN Page 12 of 12